Changes in version 0.1.0.9000                      

  - Added get_harvard_oxford_atlas() and registry entries for
    Harvard-Oxford cortical, subcortical, and combined structural
    parcellations. The default source is TemplateFlow, with threshold
    and resolution options for maximum-probability dseg images.
  - Added get_fsl_atlas() for FSL XML-described atlases, including the
    documented offset between probabilistic XML label indices and
    max-probability summary image label values. Added a thin FSL-backed
    wrapper for Julich-Brain / Brodmann-style cytoarchitectonic labels
    (get_julich_brain_atlas()), which now downloads the Nilearn/NITRC
    Juelich.tgz archive into a local FSL-style cache when FSLDIR is
    unset.
  - plot_brain(overlay = <NeuroVol>) now propagates missing data through
    the volume-to-surface projection: vertices that fall outside the
    input volume's coverage (or whose neighbourhood contains no finite
    source voxel) are emitted as NA rather than 0. Faces with no finite
    vertices are dropped from the polygon set, so uncovered cortex
    renders as transparent background instead of an opaque dark-palette
    wash. Faces with partial coverage continue to render using the
    average of their finite vertices. The internal vol_to_surf() fill
    argument changed from 0 to NA_real_.
  - plot_brain(overlay = <NeuroVol>) now repairs legacy SurfaceGeometry
    objects on the fly. The bundled data(fsaverage) artefact and the
    @geometry slots inside packaged surface atlases were serialized
    before neurosurf::SurfaceGeometry gained the label and surf_to_world
    slots; accessing those slots on a legacy object errored out and
    caused vol_to_surf() to silently return all-NA overlays.
    .resolve_overlay_surface_pair() now rebuilds any geometry that fails
    validObject() via the current constructor before passing it to
    vol_to_surf().
  - Added a canonical new_atlas() / new_surfatlas() constructor that
    assembles every loader's return value (Schaefer, Glasser, ASEG,
    Olsen MTL / hippocampus, TemplateFlow subcortical). The constructor
    validates required fields with a typed
    neuroatlas_error_invalid_atlas condition, normalises RGB colour maps
    to a data frame, builds roi_metadata uniformly, and attaches
    atlas_ref / provenance in one place — removing ~100 lines of
    per-loader boilerplate.
  - Added a lightweight atlas registry (register_atlas()) exposed via
    two new public helpers: list_atlases() enumerates the built-in
    atlases, and get_atlas(name, ...) dispatches to the registered
    loader by id or alias (e.g. get_atlas("schaefer2018", parcels="100",
    networks="7")).
  - Added centralised download helpers (.neuroatlas_download(),
    .neuroatlas_try_download()) used by the Schaefer and Glasser
    loaders. Failures now raise classed neuroatlas_error_download
    conditions with the upstream URL instead of returning a silent NULL;
    Git LFS pointer stubs are detected and reported explicitly.
  - Atlas loaders now emit cli::cli_abort() / cli::cli_warn() with
    structured classes (neuroatlas_error_*, neuroatlas_warn_*) in place
    of bare stop() / warning(), so callers can catch loader errors by
    class.
  - Added atlas provenance descriptors via new atlas_ref infrastructure:
    new_atlas_ref(), atlas_ref(), atlas_family(), atlas_space(),
    atlas_coord_space(), and validate_atlas_ref().
  - Atlas constructors now attach structured provenance/space metadata
    and compatibility aliases (space, template_space, coord_space,
    confidence) for Schaefer, Glasser, ASEG, Olsen MTL/hippocampus, and
    TemplateFlow subcortical atlases.
  - get_glasser_atlas() now accepts a source argument and defaults to
    source = "mni2009c" with fallback to legacy xcpengine when
    unavailable. Fallback paths are tagged with confidence =
    "uncertain".
  - Added test-atlas-ref.R coverage for atlas reference metadata and
    basic cross-representation label concordance checks.
  - Added space-level transform planning utilities backed by
    inst/extdata/transform_registry.csv: space_transform_manifest(),
    atlas_transform_plan(), and scope-aware atlas_transform_manifest().
  - atlas_alignment() now consults the space transform registry for
    same-representation cross-template routes (e.g., NLin6Asym
    to 2009cAsym) and reports route-specific status/confidence.
  - Fixed white gaps ("shards") in plot_brain() surface rendering caused
    by inconsistent triangle winding in some meshes.
  - Added silhouette* and network_border* options to plot_brain() for
    improved boundary styling (silhouette outline and between-network
    borders).
  - Improved plot_brain() aesthetics with smoother boundary rendering
    (border_geom = "path") and an optional normal-based shading overlay
    (shading*, fill_alpha).

                        Changes in version 0.1.0                        

  - Initial CRAN submission
  - Added support for multiple neuroimaging atlases:
      - Schaefer cortical parcellations (100-1000 parcels, 7/17
        networks)
      - Glasser multi-modal parcellation (360 regions)
      - FreeSurfer ASEG subcortical segmentation
      - Olsen medial temporal lobe atlas
  - Integrated TemplateFlow support for standardized templates
  - Added visualization support via ggseg and echarts4r
  - Implemented atlas operations: ROI extraction, data reduction,
    resampling
  - Added comprehensive vignettes and documentation